Orthopaedic disorders are a leading cause of disability in the U.S., with arthritis and/or spine problems adversely affecting quality of life fo more than 20% of adults. While advances in diagnostic imaging have greatly improved our ability to detect structural changes in musculoskeletal tissues, they typically reveal little about joint function. There is evidence that abnormal mechanical joint function contributes significantly to the development and progression of many types of joint disease. There is, therefore, a significant clinical need for the widespread use of technologies that can identify subtle abnormalities in joint function that, if left untreated, can compromise long-term joint health. Dynamic Stereo X-ray (DSX) is the only currently available technology that can achieve sub-mm bone pose (position and orientation) estimation accuracy during a wide variety of functional movements. Over the past 15 years, Dr. Tashman has developed a sophisticated set of DSX software tools for his research involving the tracking of bones during various movements. In Phase I we implemented published key algorithms of the DSX in a modern development environment and added several important innovations that make it a better clinical tool. We used motion capture data from a 3D video-based system to seed the tracking optimization. We improved the operator interaction to manipulate seed poses manually. We designed and implemented a 4D algorithm, based on a global solution finder, that uses all time frames simultaneously. These innovations reduce the amount of operator time required to process a data set, reduce the noise in the solutions, and allow the use of asynchronous X-ray systems, which are much more common than synchronous systems. These innovations have been an important step toward making DSX software a robust clinical tool. Building on our success in Phase I, in Phase II we will introduce several innovations that will enable more regions of the body to be analyzed, and further reduce the amount of operator time and CPU time needed to analyze a movement. We will implement Dr. Tashman's published hierarchical algorithm in the 4D optimization to better track bones that overlap significantly with other bones (e.g., the spine) and to extend this algorithm to other regions of the body. We will also develop a modular system for defining anatomically meaningful coordinate systems in any bone, which is needed to represent joint kinematics of the tracked bones. We will quantify the robustness of the solution to inaccuracies in the input to provide guidelines for the required accuracy of the seed pose. Finally, we will implement the remaining DSX algorithms, including 3D calibration and distortion correction, to create a complete clinical package.